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KMT2C lysine methyltransferase 2C [ Homo sapiens (human) ]

Gene ID: 58508, updated on 18-Sep-2024

Summary

Official Symbol
KMT2Cprovided by HGNC
Official Full Name
lysine methyltransferase 2Cprovided by HGNC
Primary source
HGNC:HGNC:13726
See related
Ensembl:ENSG00000055609 MIM:606833; AllianceGenome:HGNC:13726
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
HALR; MLL3; KLEFS2
Summary
This gene is a member of the myeloid/lymphoid or mixed-lineage leukemia (MLL) family and encodes a nuclear protein with an AT hook DNA-binding domain, a DHHC-type zinc finger, six PHD-type zinc fingers, a SET domain, a post-SET domain and a RING-type zinc finger. This protein is a member of the ASC-2/NCOA6 complex (ASCOM), which possesses histone methylation activity and is involved in transcriptional coactivation. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in thyroid (RPKM 8.7), bone marrow (RPKM 8.5) and 25 other tissues See more
Orthologs
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Genomic context

See KMT2C in Genome Data Viewer
Location:
7q36.1
Exon count:
59
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (152134925..152436003, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (153307815..153608900, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (151832010..152133088, complement)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene polypeptide N-acetylgalactosaminyltransferase 11 Neighboring gene small nucleolar RNA U13 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:151778343-151779337 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr7:151804574-151805773 Neighboring gene uncharacterized LOC731075 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26876 Neighboring gene Y-box binding protein 1 pseudogene 4 Neighboring gene MPRA-validated peak6855 silencer Neighboring gene Sharpr-MPRA regulatory region 15588 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26877 Neighboring gene septin 7 pseudogene 6 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr7:152091085-152091724 Neighboring gene Sharpr-MPRA regulatory region 5889 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26878 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26879 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26880 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26881 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18830 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18831 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18832 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18833 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:152138204-152138404 Neighboring gene fatty acid binding protein 5 pseudogene 3 Neighboring gene chaperonin containing TCP1 subunit 8 like 1, pseudogene

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Kleefstra syndrome 2
MedGen: C4540395 OMIM: 617768 GeneReviews: Not available
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated 2018-01-24)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated 2018-01-24)

ClinGen Genome Curation PagePubMed

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • FLJ12625, FLJ38309, KIAA1506, MGC119851, MGC119852, MGC119853, DKFZp686C08112

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
 
enables RNA binding HDA PubMed 
enables acyltransferase activity IEA
Inferred from Electronic Annotation
more info
 
enables histone H3K4 methyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
 
enables histone H3K4 methyltransferase activity IDA
Inferred from Direct Assay
more info
PubMed 
enables histone H3K4 monomethyltransferase activity IEA
Inferred from Electronic Annotation
more info
 
enables histone H3K4 trimethyltransferase activity IEA
Inferred from Electronic Annotation
more info
 
enables histone methyltransferase activity IDA
Inferred from Direct Assay
more info
PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables transcription coactivator activity IBA
Inferred from Biological aspect of Ancestor
more info
 
Process Evidence Code Pubs
involved_in chromatin remodeling IEA
Inferred from Electronic Annotation
more info
 
involved_in methylation IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in protein-containing complex organization IEA
Inferred from Electronic Annotation
more info
 
involved_in response to electrical stimulus IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
part_of MLL3/4 complex IBA
Inferred from Biological aspect of Ancestor
more info
 
part_of MLL3/4 complex IDA
Inferred from Direct Assay
more info
PubMed 
part_of MLL3/4 complex IPI
Inferred from Physical Interaction
more info
PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
 
part_of histone methyltransferase complex IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 
located_in nucleoplasm TAS
Traceable Author Statement
more info
 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
histone-lysine N-methyltransferase 2C
Names
ALR-like protein
histone-lysine N-methyltransferase MLL3
histone-lysine N-methyltransferase, H3 lysine-4 specific
homologous to ALR protein
lysine (K)-specific methyltransferase 2C
myeloid/lymphoid or mixed-lineage leukemia protein 3
NP_733751.2

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_033948.1 RefSeqGene

    Range
    5003..306081
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_170606.3NP_733751.2  histone-lysine N-methyltransferase 2C

    See identical proteins and their annotated locations for NP_733751.2

    Status: REVIEWED

    Source sequence(s)
    AF264750, AK025911, AY024361, BP281562, BU623509, BU685177, CD513584
    Consensus CDS
    CCDS5931.1
    UniProtKB/Swiss-Prot
    Q8NC02, Q8NDF6, Q8NEZ4, Q9H9P4, Q9NR13, Q9P222, Q9UDR7
    UniProtKB/TrEMBL
    A0A7P0TAI3
    Related
    ENSP00000262189.6, ENST00000262189.11
    Conserved Domains (17) summary
    smart00317
    Location:47724893
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    smart00508
    Location:48954911
    PostSET; Cysteine-rich motif following a subset of SET domains
    COG2940
    Location:47254911
    SET; SET domain-containing protein (function unknown) [General function prediction only]
    sd00025
    Location:10841106
    zf-RanBP2; RanBP2-type Zn finger [structural motif]
    cd15509
    Location:343388
    PHD1_KMT2C_like; PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D)
    cd15511
    Location:466517
    PHD3_KMT2C; PHD finger 3 found in Histone-lysine N-methyltransferase 2C (KMT2C)
    cd15513
    Location:10091055
    PHD5_KMT2C_like; PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in KMT2D
    cd15594
    Location:390435
    PHD2_KMT2C; PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C)
    cd15596
    Location:9521008
    PHD4_KMT2C; PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C)
    cd15600
    Location:10861136
    PHD6_KMT2C; PHD finger 6 found in Histone-lysine N-methyltransferase 2C (KMT2C)
    cd15696
    Location:247330
    ePHD1_KMT2C; Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C)
    cd15697
    Location:44024506
    ePHD2_KMT2C; Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C)
    pfam05964
    Location:45524602
    FYRN; F/Y-rich N-terminus
    pfam05965
    Location:46084689
    FYRC; F/Y rich C-terminus
    pfam11176
    Location:16921775
    DUF2962; Protein of unknown function (DUF2962)
    pfam15233
    Location:31813270
    SYCE1; Synaptonemal complex central element protein 1
    cl00082
    Location:16541705
    HMG-box; High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I ...

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    152134925..152436003 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    153307815..153608900 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_021230.2: Suppressed sequence

    Description
    NM_021230.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.